Contacts of the helix formed by residues 542 - 554 (chain C) in PDB entry 6NYY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 542 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500C LEU* 3.5 25.4 - - + +
505C LEU* 4.4 15.7 - - + -
508C LYS* 3.5 40.2 - - + +
509C LEU* 5.9 2.5 - - + -
512C LEU* 5.3 1.8 - - + +
541C ASN* 1.3 73.8 - - - +
543C LYS* 1.3 63.9 + - + +
544C HIS 3.1 3.4 + - - -
545C PHE* 3.2 19.7 + - + +
546C GLU* 3.5 27.7 + - + +
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Residues in contact with LYS 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541C ASN* 3.3 8.2 - - + +
542C GLN* 1.3 78.4 - - + +
544C HIS* 1.3 65.7 + - + +
545C PHE 3.5 0.2 - - - -
546C GLU* 4.1 25.1 + - - +
547C GLN* 3.3 33.8 + - - +
737C ASP* 5.2 9.5 + - - -
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Residues in contact with HIS 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528C ALA* 3.3 30.1 - - - +
531C ILE* 4.2 16.6 + - + +
532C ALA* 3.3 25.4 - - - +
535C HIS* 5.1 8.6 + + + +
537C SER* 3.7 25.4 - - - -
539C SER 4.5 0.7 - - - -
540C ILE* 4.0 3.8 - - + -
541C ASN* 3.5 44.0 + - + +
542C GLN 3.1 1.4 - - - -
543C LYS* 1.3 88.4 - - + +
545C PHE* 1.3 60.9 + - - +
546C GLU 3.4 0.2 - - - -
547C GLN* 3.7 12.3 + - - +
548C ALA* 3.3 12.0 + - - +
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Residues in contact with PHE 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491C LEU* 3.6 32.5 - - + -
494C LEU* 3.9 11.4 - - + -
496C LEU* 3.7 15.7 - - + -
500C LEU* 5.5 0.2 - - + -
505C LEU* 3.6 20.2 - - + -
509C LEU* 3.7 32.5 - - + -
524C VAL* 3.7 15.1 - - + +
525C CYS* 4.4 3.1 - - - -
528C ALA* 3.5 19.5 - - + -
540C ILE* 3.6 15.9 - - + -
541C ASN 3.2 27.4 - - - -
542C GLN* 3.2 12.8 + - + +
544C HIS* 1.3 77.4 - - - +
546C GLU* 1.3 60.5 + - + +
548C ALA* 2.9 18.1 + - - +
549C ILE* 2.9 18.9 + - - +
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Residues in contact with GLU 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508C LYS* 5.3 1.7 - - - -
509C LEU* 6.0 0.2 - - + -
512C LEU* 4.1 28.6 - - + +
542C GLN* 3.5 31.1 + - + +
543C LYS* 4.1 28.9 + - - +
544C HIS 3.4 0.4 - - - -
545C PHE* 1.3 77.2 - - + +
547C GLN* 1.3 58.5 + - + +
549C ILE* 3.8 8.9 - - + +
550C GLU* 3.2 43.2 + - - +
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Residues in contact with GLN 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531C ILE* 3.3 42.0 - - + +
534C ARG* 5.3 1.2 + - - -
535C HIS* 4.6 7.5 - - - -
543C LYS* 3.3 24.6 + - - +
544C HIS* 4.0 8.4 - - - +
545C PHE 3.2 0.6 - - - -
546C GLU* 1.3 78.0 - - + +
548C ALA* 1.3 58.8 + - - +
550C GLU* 4.2 10.3 - - - +
551C ARG* 3.5 18.0 + - - +
593C LYS* 5.6 5.5 - - - +
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Residues in contact with ALA 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524C VAL* 3.8 22.6 - - - +
527C GLU* 3.8 10.7 - - + +
528C ALA* 3.6 28.3 - - + +
531C ILE* 4.1 3.8 - - - -
544C HIS 3.3 8.4 + - - +
545C PHE 2.9 9.9 + - - +
547C GLN* 1.3 78.5 - - - +
549C ILE* 1.3 64.0 + - - +
551C ARG* 4.0 4.4 + - - +
552C VAL* 3.3 25.6 + - - +
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Residues in contact with ILE 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509C LEU* 4.6 7.2 - - + -
512C LEU* 3.7 44.9 - - + +
513C THR* 3.7 18.8 - - + -
516C PHE* 5.0 2.4 - - + -
524C VAL* 3.7 24.7 - - + -
545C PHE 2.9 17.5 + - - +
546C GLU* 3.4 11.2 + - - +
548C ALA* 1.3 78.2 - - - +
550C GLU* 1.3 61.0 + - + +
552C VAL* 3.0 7.6 + - - +
553C ILE* 3.0 48.9 + - + +
607C GLN* 4.2 10.8 - - - +
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Residues in contact with GLU 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546C GLU* 3.2 26.4 + - - +
547C GLN* 4.8 6.3 - - - +
549C ILE* 1.3 76.4 - - + +
551C ARG* 1.3 57.6 + - - +
553C ILE* 4.5 0.7 - - - +
554C GLY* 2.9 28.5 + - - +
555C GLY 3.7 1.2 + - - -
592C LEU* 5.5 1.7 - - - +
593C LYS* 3.0 51.1 + - - +
599C ARG* 3.3 28.1 + - - +
605C TYR* 4.9 0.2 - - - -
607C GLN* 3.5 34.5 - - - +
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Residues in contact with ARG 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527C GLU* 4.3 15.0 - - - +
531C ILE* 5.4 4.0 - - + -
547C GLN 3.5 18.6 + - - +
548C ALA* 4.2 6.5 - - - +
549C ILE 3.2 0.8 - - - -
550C GLU* 1.3 80.6 - - - +
552C VAL* 1.3 63.4 + - + +
554C GLY 3.7 0.9 + - - +
555C GLY* 3.6 35.8 - - - -
556C LEU* 3.6 14.0 - - - +
599C ARG* 5.2 1.1 - - - +
319D GLU* 2.6 43.9 + - - +
471D ARG* 4.4 8.2 - - - +
472D GLN* 2.9 43.5 + - - +
473D ILE* 4.1 2.2 - - - +
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Residues in contact with VAL 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516C PHE* 4.8 16.8 - - + -
520C ASP* 5.8 6.3 - - + +
523C ASN* 4.8 15.3 - - + +
524C VAL* 5.0 6.1 - - + +
527C GLU* 3.8 20.4 - - - +
548C ALA 3.3 17.0 - - - +
549C ILE* 3.0 7.8 + - - +
551C ARG* 1.3 81.0 - - + +
553C ILE* 1.3 65.4 + - - +
554C GLY 3.9 3.1 - - - +
466D PRO* 5.4 13.0 - - + -
470D ASP 5.7 2.0 - - - +
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Residues in contact with ILE 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512C LEU 5.1 4.5 - - - +
513C THR* 6.0 0.9 - - - -
514C PRO* 6.0 3.4 - - + +
516C PHE* 3.8 28.9 - - + -
549C ILE* 3.0 36.8 + - + +
552C VAL* 1.3 78.3 - - - +
554C GLY* 1.3 64.1 + - - +
607C GLN* 4.0 24.7 - - - +
608C TYR 5.8 0.9 - - - +
610C PRO* 6.4 0.7 - - + -
2I ALA* 3.7 32.5 - - + -
3I ALA* 4.4 13.6 - - + +
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Residues in contact with GLY 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550C GLU 2.9 15.1 + - - -
551C ARG* 3.7 6.6 + - - +
552C VAL 3.9 3.5 - - - +
553C ILE* 1.3 85.3 - - - +
555C GLY* 1.3 58.5 + - - -
599C ARG* 4.1 10.3 - - - -
600C GLY* 5.3 2.9 - - - -
605C TYR* 6.1 4.7 - - - -
607C GLN* 5.1 2.2 + - - -
3I ALA* 6.0 3.6 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il